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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatagcctgtttgccccttgagatctatggactgttgaccttatgcatgttttattttctttgcag

Basic information

species Zea mays
transcript GRMZM2G169694_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 2
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac---tactactgcattcatagcctgtt----tgccccttgagatctatggactgttgaccttatgcatgttttattttctttgcag---
||||| || |||||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||||| || |   |  | |||||||   ||   |||    | | ||||| ||           || | ||||||||| || |||||| ||| | |   
GCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTGgtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcatt-atcttatgcattttgtatttttttttctgcag

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 2
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatagcctgtttgccccttgagatctatggactgttgaccttatgcatgtt-ttattttctttgcag--------------------------------------------------
|| |||||||||||||||||  | ||||| || ||||| ||||||||| |||||||  | || || || ||||| | ||     |  || |        | |   |    |   | | |  ||   |   |    | | ||    |||| ||  |  |                                                    
GCCACGATTGGTATTGATTTTTTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGGCTGCAGCTgtggtaagatgtggcatcttggaaattctatccgaaaggaaataatggtattggggacgaaaagggaagggattcccttatcttgatcccttatcatataatttaggagttatcttttattagggatttgacttgcaatcag

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 2
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcat-tcatagc--ctgtttgccccttgagat--ctatggactgttga---ccttatgcatgttttattttctttgcag-----
||||| |||||||||||||| || ||||| || ||||| ||||||||| |||||||  |||| ||  | ||||| | | |      | |||| ||||||     || |      | | ||    | | | ||   |     ||| | | |  ||        |         
GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagat-atgggaccagcatctcatagtaatagtataaattataaaatggtcaggaaatgaaaagggttttaggaaaggattggaagaagtaggatcatg

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggt-----gactactactgcattcatagcctgtt---tgccccttgagatc---tatggactgttgaccttatgcatgttttattttctttgcag
|| || |||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | ||||| | |     | ||  | |    |||  |  |||     |  |  |  |||||   | | ||   || || |   |   |    | |    |  |||
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgaga--gccgaaatcatatgacag

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 2
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatag-cctgtttgccccttgagatct-----atggactgttgacctt---atgcatgttttattttctttgcag---
||||| |||||||| ||||| || |||||||| ||||||||||||||| | || ||  |  | ||||||||||  | |      |  ||      ||| ||||||||    |   | ||      ||  | | ||| |  |   ||        |||||  |||       
GCTACTATTGGTATCGATTTTCTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagattttagttcttgatgctttagacctgtttgtatatattgctcccacaaatatatttttgtctctcccatttcaaaaatatttattttctgaagt

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 5'ss of exon 2
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgc--attcatagcctgtttgccccttgagatcta-tggactgttgaccttatgcatgttttattttctttgcag---------
||||| ||||||||||||||||| |||||||| ||||| ||||||||| |||| ||  | || ||  | |||||  |   |  | |||    ||| || ||   | |   |     | | |  || ||| |||    | | |   | |  |||| |||             
GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTGgtaaagatccagcaactaataatttattgcaaatatctacagatgggtgtggtgaacttttgtttcttttcccttctccttttttttttttttttttttg

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 3
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatagc-ctgtttgccccttg-agatctatggactgttgaccttatgcatgtt---ttattttctttgcag
|| || || |||||||| |||||||||||||| ||||||||||| ||  | |||||| | || || |||||||   |    | |||||| |      || || |  |  ||| | |  ||  ||| | |     || | |  ||||       |   | |||||
GCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTGgtg-agcacttgctactggacagccggcgctatcagtgcctcgcacgtcgttggtcag--agtctcacgtgtgttggcccgctgcgtgtgcag

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatagcctgtttgccccttg-agatctatggactgttgaccttatgcatgttttattttct--ttgcag----------
|| || ||||| |||||||| || ||||| |||||||||||||||||  | || ||| | || || || |||||   |  |||  | |   |   |    |     |    || | ||        |  ||    | | |  |||||| | | |   | ||           
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgta-actttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211199864|gb|FK959366.1|FK959366
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCACGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|32919616|gb|CF024428.1|CF024428
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|148970042|gb|EE020962.2|EE020962
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|33093555|gb|CF053549.1|CF053549
EST:     ACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: ACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|149085277|gb|EE174782.2|EE174782
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|89251359|gb|DY623145.1|DY623145
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCCAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|71333158|gb|DR803614.1|DR803614
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|56462112|gb|CK986410.1|CK986410
EST:     ACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: ACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|148960910|gb|EE011595.2|EE011595
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|211199857|gb|FK959359.1|FK959359
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGA
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGA
EST: gi|87152147|gb|DY396936.1|DY396936
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|32870836|gb|CF010518.1|CF010518
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
EST: gi|149085276|gb|EE174781.2|EE174781
EST:     CTGTCAAAGACAATGTCCCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 232

GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgac ... ttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatagcctgtttgccccttgagatctatggactgttgaccttatgcatgttttattttctttgcag

- - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -  TGAAGA